gridss: remove redundant collectGridssMetrics

1 files changed, 0 insertions, 34 deletions

diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
deleted file mode 100644
index 91e04c7..0000000
--- a/tools/gridss-collectGridssMetrics.nix
+++ /dev/null
@@ -1,34 +0,0 @@
-{ bionix
-, nixpkgs
-, thresholdCoverage ? 10000
-, flags ? null
-, config ? null
-}:
-
-with nixpkgs;
-with lib;
-with bionix.types;
-
-input:
-
-let
-  ref = matchFiletype "gridss-collectGridssMetrics" { bam = x: x.ref; } input;
-  sorted = matchFileSorting "gridss-collectGridssMetrics" { name = _: true; } input;
-in
-
-
-stdenv.mkDerivation rec {
-  name = "gridss-collectGridssMetrics";
-  buildInputs = [ jre ];
-  buildCommand = ''
-    mkdir $out
-    ln -s ${input} input.bam
-    java -Xmx1G -cp ${bionix.gridss.jar} \
-			gridss.analysis.CollectGridssMetrics \
-			${optionalString sorted "ASSUME_SORTED=true"} \
-      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
-			I=input.bam \
-			O=$out \
-			THRESHOLD_COVERAGE=${toString thresholdCoverage}
-    '';
-}